GapMind for catabolism of small carbon sources

 

Alignments for a candidate for icd in Sphingomonas koreensis DSMZ 15582

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate Ga0059261_0194 Ga0059261_0194 isocitrate dehydrogenase (NADP) (EC 1.1.1.42)

Query= BRENDA::A5U813
         (409 letters)



>FitnessBrowser__Korea:Ga0059261_0194
          Length = 407

 Score =  603 bits (1554), Expect = e-177
 Identities = 294/405 (72%), Positives = 338/405 (83%), Gaps = 3/405 (0%)

Query: 6   KIKVSGPVVELDGDEMTRVIWKLIKDMLILPYLDIRLDYYDLGIEHRDATDDQVTIDAAY 65
           KIKV  PVVE+DGDEMTR+IW+ I++ LI PYLDI L YYDLG+E RD T+DQ+T+DAA 
Sbjct: 3   KIKVKNPVVEIDGDEMTRIIWEWIRERLIKPYLDIDLKYYDLGVEKRDETNDQITVDAAN 62

Query: 66  AIKKHGVGVKCATITPDEARVEEFNLKKMWLSPNGTIRNILGGTIFREPIVISNVPRLVP 125
           AIK+ GVGVKCATITPDEARVEEFNLK+MW SPNGTIRNILGG +FREPIVISNVPRL+P
Sbjct: 63  AIKEFGVGVKCATITPDEARVEEFNLKEMWKSPNGTIRNILGGVVFREPIVISNVPRLIP 122

Query: 126 GWTKPIVIGRHAFGDQYRATNFKVDQPGTVTLTFTPADGSAPIVHEMVSIPEDGGVVLGM 185
           GWTKPIV+GRHAFGDQYRAT+ K+  PG + L F  ADG   I  E+ + P  G V + M
Sbjct: 123 GWTKPIVVGRHAFGDQYRATDVKIPGPGKLRLVFEGADGEV-IDREVFNFPSSG-VAMAM 180

Query: 186 YNFKESIRDFARASFSYGLNAKWPVYLSTKNTILKAYDGMFKDEFERVYEEE-FKAQFEA 244
           YN  +SIRDFARASF+YGLN KWPVYLSTKNTILKAYDG FKD F+ V++ E FK +F  
Sbjct: 181 YNLDDSIRDFARASFNYGLNLKWPVYLSTKNTILKAYDGRFKDLFQEVFDNEGFKEKFAE 240

Query: 245 AGLTYEHRLIDDMVAACLKWEGGYVWACKNYDGDVQSDTVAQGYGSLGLMTSVLMTADGK 304
           AG+ YEHRLIDDMVA+ LKW G +VWACKNYDGDVQSD VAQG+GSLGLMTSVL++ DGK
Sbjct: 241 AGIVYEHRLIDDMVASALKWSGEFVWACKNYDGDVQSDQVAQGFGSLGLMTSVLLSPDGK 300

Query: 305 TVEAEAAHGTVTRHYRQYQAGKPTSTNPIASIFAWTRGLQHRGKLDGTPEVIDFAHKLES 364
           TVEAEAAHGTVTRHYRQ+Q GK TSTNPIASIFAWT GL+ RGK D TPEV+ FA  LE 
Sbjct: 301 TVEAEAAHGTVTRHYRQHQQGKATSTNPIASIFAWTGGLKFRGKFDETPEVVKFAETLER 360

Query: 365 VVIATVESGKMTKDLAILIGPEQDWLNSEEFLDAIADNLEKELAN 409
           V I TVESGKMTKDLA+LIGP+Q W+ +E+F +AI +NLE E+A+
Sbjct: 361 VCIETVESGKMTKDLALLIGPDQPWMTTEQFFEAIRENLETEMAS 405


Lambda     K      H
   0.318    0.136    0.409 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 643
Number of extensions: 19
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 409
Length of database: 407
Length adjustment: 31
Effective length of query: 378
Effective length of database: 376
Effective search space:   142128
Effective search space used:   142128
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate Ga0059261_0194 Ga0059261_0194 (isocitrate dehydrogenase (NADP) (EC 1.1.1.42))
to HMM TIGR00127 (isocitrate dehydrogenase, NADP-dependent (EC 1.1.1.42))

Software error:

../bin/blast/fastacmd -i /tmp/list.14864.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14864.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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